New Family, New Beginings
by RAandLRforever
Summary: Sequel to A Mistake A Baby A Boyfriend. The twins are normal and healthy little babies. Rory and Jess buy a house in a small town between Hartford and Stars Hallow. And many crazy things happen what will the new family do?
1. New Family, New Beginings

A/n: Hello again! Hope you enjoy the sequel to A Mistake, a Baby, a Boyfriend. 

Disclaimer: I sadly do NOT own any of these incredible and sometimes insane characters. I only own Mary and Lucas. Enjoy!

**New Family, New Beginnings**

"Rory…Rory… wake up." a very groggy Jess groaned to his girlfriend lying in bed beside him.

"Humph?" Rory moaned.

"The babies are crying and its your turn." Jess said turning to a new position covering his ears with his pillow.

Rory groaned and looked at the clock beside the bed.

"3:00! What do you mean my turn I just fed them and changed them an hour ago I believe Mr. Mariano that it is your turn to tend to your kids." she said groaning and lying back.

"They're your kids from 8pm-6am." he said his voice muffled from under the pillow.

"I don't believe you Jess!" Rory groaned sitting up and hitting Jess with a pillow. She slipped on her bunny slippers and padded off towards the opposite side of the room where the twins were crying for their parents. Rory may have to tend to her children, and she truly didn't mind, but she wasn't going to let Jess off the hook that easily. She purposely made as much noise and she could change Mary and Lucas' diapers and getting the bottles ready.

"Here give me Mary." Jess murmured coming up behind Rory and taking his 3 month old daughter in his arms.

"Thanks for the help." Rory said yawning and rocking Lucas in the rocking chair.

"Well I Have to be at Luke's at 4 because we have an early delivery so I needed to get up. "

"Jess its time to get up." Luke grumbled from the other side of the door.

"Its ok Luke were up." said Jess just loud enough for Luke to hear but quiet enough not to wake the now sleeping babies.

"Well I better go get my shower." Jess said putting Mary in her crib and kissing Rory and Lucas.

"Alright well I'm going back to bed." she said putting Lucas beside his sister.

"Alright see you later." he said rapping her in a passionate hug.

"I love you Jess Mariano." she said kissing him a simple kiss.

"I love you Rory Gilmore." he said giving her a more passionate kiss.

After Rory shooed her loving boyfriend away to work she settled back in to bed. They were still living with Lorelai and Luke since Rory was still knew at the whole mother job. It was so strange laying in her old bedroom. She looked around and noticed all the changes. All the baby stuff that filled the room. The larger bed for her and Jess to share and the of course the crib and babies. Even though the room had changed it was still the same that all the past memories came flooding back to her. Like all the slumber parties with Lane, the arguments with her mom, and even the first time she'd ever made love, with Dean of all people. As she thought of all the fond memories she knew this was the life she may not have always planed but it was the one she wanted. Just as Rory was about to scream she heard her mother screaming her name at the top of her lungs.

"Rory! Oh my gosh! Rory!" Lorelai yelled stomping down the stairs.

"What?" she hollered back wincing for she was hoping not to wake up her sleeping children.

"Rory!" Lorelai laughed and screamed as she jumped on Rory's bed grabbing her in a big hug. "I'm pregnant!"

"What! Oh my gosh Mom! I so happy!" Rory yelled back grabbing her in a big hug and the two started crying.

"I can't believe it. I'm so happy Rory."

"I am to Mom. Wow."

The two looked at each other and squealed again now waking the twins.

"I'm sorry Rory." Lorelai said getting up and picking up her crying grandson.

"It's alright." Rory said picking up her daughter.

"I can't believe in nine months I'll have one of these." Lorelai said rocking Lucas back and forth in her arms.

"Have you told Luke yet?"

"No I just now took the test. I better call him." Lorelai rambled putting down Lucas and running for the phone.

Rory shook her head at her mother and smiled as a realization came to her. They were going to have to move out so her new sibling could have her room.

"Joy. Another adventure." she sighed to herself but as she heard her mom crying and laughing in the living room she knew it was her time.


	2. Im So Sorry Daddy Part 1

**Disclaimer: **I do not own anything Gilmore Girls. If I did I would not be sitting here. duh

**A/N: **Thanks for all the feedback and ideas. I really have no idea where this is going so I need all the help I can get.Well r&r.

**I'm So Sorry Daddy Part 1**

Rory put Mary in her crib beside her sleeping brother and walked to the kitchen for a cup of coffee. She got out a blue mug and poured her lifeline into the cup. She grabbed the newspaper laying on the counter and had a seat at the table. She turned to the real state part of the paper. She skimmed the houses dismissing the ones to far from Stars Hallow, or ones she knew that Jess and her wouldn't like. As she got to the end of the page she saw the perfect house. It was right between Hartford and Stars Hallow and it was in their price range. She was so involved in the house plans she didn't notice Lorelai sneaking up behind her.

"Why are you looking at houses? Are you thinking of moving out?" her mother asked pouring her a cup of coffee as well.

"No… well… maybe." Rory said folding up the paper and putting it on the chair beside her.

"But why? I thought you were going to stay year for at least a year." Lorelai said looking hurt.

"Well it's not official yet. I mean I haven't even talk to Jess yet. I just was thinking about you expecting now and you'll need my room for the baby and I think it's time mom. Jess is 22 and I will be in a week so we need to get on with our lives." Rory said playing with her coffee trying to convince herself as well as Lorelai.

"I understand I'm just going to miss you and the kids." Lorelai said hugging her daughter.

"What about Jess?" Rory said smirking.

"I said kids didn't I?" Lorelai said smiling.

"Mom." Rory said laughing.

They continued to giggle as Rory's cell began to ring. She ran into her room and grabbed the razor from her purse.

"Hello?" she asked not recognizing the number.

"Rory? This is Grandma Hayden. Your father is in the hospital. It doesn't look good. You better get down here."

"Oh my gosh! What happened?" Rory yelled causing Lorelai to walk in to see what was wrong.

"He was in some type of accident. You just better get down here."

"Okay I'll be there as fast as I can." Rory said closing her phone and rushing to her closet.

"Rory what's wrong." Lorelai said walking after her daughter.

"It's dad. He's in the hospital. I need to go see him." she said grabbing jeans and a sweat shirt.

"Is he okay?" Lorelai asked.

"I don't know."

"Do you want me to watch the kids?" her mother asked.

"No, I need to bring them with me. He's dying and he's never seen his grandkids. He needs to see them." Rory said grabbing the diaper bags and filling them with the necessities.

"Of course. Do you want me to call Jess?"

"Yes. Please." Rory replied.

With that Lorelai went to the kitchen to call the men. Rory grabbed warm clothes for the twins and dressed them and put them in their punkin seats.

"Hey babe." she heard Jess say.

She turned to see him in the doorway.

"Oh Jess." she turned to him sobbing.

He wrapped her in a hug and told her it would be okay.

"I'm a horrible daughter, Jess. I never let him see Mary and Lucas. And the last time I ever saw him I told him I hated him and for him to stay out of my life." she said sobbing harder.

"Rory, you know you have been the best daughter under the circumstances. He loves you I know he does. He just doesn't like me that's all. Come on lets go." he said grabbing the punnkin seats and giving Rory a kiss on the forehead.

Rory followed Jess out to the living room where Luke and Lorelai were sitting on the couch.

"Do you want us to go hun?" Lorelai asked.

Rory simply nodded her head and the family headed toward the cars. The car ride to the hospital was silent. Rory kept think of Lorelai and Luke's wedding reception where she had had a fight with Christopher. She had found out about what he was trying to do earlier that day in Lorelai's dressing room and she just lost it. She had told no one, not even Jess about the painful exchange the father and daughter had had behind Miss Patty's dance studio.

_Flash back… _

"_I can't believe you!" Rory yelled at her father who was walking to his car._

"_What are you talking about?" _

"_Back in the dressing room earlier. Why can't you just leave my mom alone. She's happy with Luke."_

"_I know but I love her Rory. We should be together. I mean look at what your kids are gonna think when they find out that Luke isn't their Grandfather." Chris said furious._

"_It won't matter because you won't even be around anyway. You'll treat them like you treated me all my life. Only coming around when it was convenient and always hurting my mom."_

"_Get used to it babe. Jess is gonna do the same thing."_

"_What do you mean?" _

"_Look at him. He's a punk. Never finished high school, he's probably a druggy, and he will never commit."_

"_I can't believe you. Jess is perfect and I … I … I hate you. I want you out of my life and my kids' life." Rory said as she walked away never looking back with hot tears streaming down her cheeks. _

_End of flash back._

"Rory are you okay?" Jess asked as they pulled into the hospital parking lot.

"Yeah lets go."


	3. Im So Sorry Daddy Part 2

**Disclaimer: **I do not own anything Gilmore Girls

**I'm So Sorry Daddy Part 2**

Jess grabbed the car seats and Rory grabbed the diaper bags. They met up with Luke and Lorelai in the lobby.

"Here…I'll take these." Lorelai said taking the bags from here daughter.

Rory walked over to the information desk. Finally after a few minutes the nurse finally noticed her standing at the desk

"Can I help you?" she asked clearly not interested.

"Yeah, I'm here for my father, Christopher Hayden." Rory said her voice shaky.

"Awh yes the motorcycle man. He's in room 406."

Rory turned to go back to the lobby.

"Did you find anything out?" Jess asked.

"Yeah he's in room 406, will the twins be okay?" she asked looking at her kids.

"Yeah, sure we'll watch them. Go." Lorelai said giving her daughter a comforting smile.

Rory walked around the hospital till she found an elevator. She pushed the button for the forth floor. When it opened she walked around until she found the room labeled 406. She braced herself not knowing what to expect.

"Here it goes." she whispered.

She couldn't believe what see saw in front of her. This man couldn't possibly be here father. He was all bruised in the face and it was very swollen. His left arm was in a cast and his left leg was in weird looking air boot. He had oxegen and several iv's in his right arm. She shivered before sitting in the chair placed beside Chris's bed.

"Hey stranger." she heard a faint croak.

"Dad?" she asked somewhat not believing he was talking.

"Hey baby." he said slightly moving his head to look at his daughter.

"Oh dad I'm so sorry! I didn't mean what I said. I want you in my life, and my kids! Oh daddy I'm so sorry." Rory said cry and trying to hug her injured dad.

"Rory, honey. It's okay. I know what I did was wrong. I just thought me and your mom still had a chance until that night. After that seeing how happy she was and how happy he seemed to make her I realized I could never do that." Chris said in a hoarse whisper trying to calm Rory.

lobbylobbylobbylobbylobbylobbylobbylobbylobbylobbylobby

"I hope Chris is going to be okay… for Rory's sake." Jess said lounging back in the waiting room chair.

"Yeah me to." Lorelai said looking off into space.

Just then Rory returned to the lobby.

"So?" everyone seemed to ask at the same time.

"He's gonna be okay. He broke his arm and hurt his leg pretty bad but… he's gonna be okay." Rory said getting a hug from Jess.

"Oh kiddo that's great." Lorelai said smiling and patting her on the leg.

"Where's Luke?" Rory asked noticing her step dad wasn't with the crew.

"Oh he doesn't do hospitals and he was needed back at the diner." Jess said smirking as he remembered his uncle's face as a sick patient was rolled buy earlier.

"Oh." Rory smiled remembering her many times at the hospital that Luke conveniently disappeared.

Just then Lucas awoke from his nap.

"Awh how's my little guy?" Rory asked taking the baby boy from his punkin seat.

"Are you going to show Christopher?" Lorelai asked playing with her little grandson's toes.

"Yeah, if Jess will come with me." Rory said looking at her boyfriend with her big doe eyes.

"If you really wanna do this." Jess smirked.

"Yeah." Rory smirked. "Grab Mary please. Mom do you want to go?"

"No, this is your thing with your dad. I need to get back to the inn anyway. Michelle probably has all the employees quitting." Lorelai laughed smiling at her daughter.

"Okay. Come on Jess." Rory said standing up with her son and leading the way to the elevator.

"Good luck." whispered Lorelai winking at Jess.

"Huh?" Rory asked looking back.

"Oh nothing. Just tell him I said hi." Lorelai said trying not to laugh at being caught.

**NEXT CHAPTER: **Jess is going to ask Chris a very important question that could change the relationship.

A/N: Well I hope you like it. I had mixed emotions on killing off Christopher but I got another idea. So I hope you all enjoyed it and I would love for you all to review and tell me what you would want me to change or if you like it just let me know.


	4. Chapter 4

**Disclaimer: **I do not own anything Gilmore Girls

Chapter 4

It was about 3 in the afternoon before Jess, Rory, and the babies returned to Luke's diner. Rory carried the sleeping twins up to the apartment where they kept extra bassinettes and Jess took a seat next to Lorelai at the counter.

"So?" Lorelai grinned eying Jess.

"What?" asked Jess.

"What did he say?"

"Well I guess we have to wait on her now." Jess said pouring himself a cup of coffee.

"Wait on who for what?" asked Rory coming down the steps.

"Oh nothing." Jess smirked taking a sip of his drink.

"There is something going on Mr. Mariano and I will find out." she said stealing his cup and gulping down as much as she could.

"Just like your mother in everyway." he said sighing and walking over to the kitchen to help his uncle.

"So what do you know about all that?" Rory asked her mother sitting down beside her.

"Not much, about as much as you do." she said looking away.

"Alright if you say so." Rory said dropping the subject.

5 weeks later…..

"Rory!" yelled Lorelai.

"Huh…" Rory mumbled looking over at her alarm clock to see it was only 7 in the morning. "This better be important." she groaned walking out of her bedroom into the kitchen.

"Oh it is." said Lorelai grabbing a pop tart and heading to her room.

When they walked into her mother's room she saw clothes scattered all around the room in heaps.

"What happened here." Rory laughed.

"Well today I go to see about the baby and make sure everything is ok and I just don't know what to wear." Lorelai dramatically sighed landing on her bed with a thud.

"Just wear something comfy." Rory said walking over to her mom's closet.

"But I want to look good. I want to look like all those hot moms that can wear dress pants and be as fat as a cow." Lorelai murmured.

"Mom everyone looks beautiful pregnant, its that mothers glow. And beside your not even showing so it doesn't really matter what you wear. How about this?" Rory asked pulling out a cute blue BCBG sweat suit.

"I guess. Oh Rory I don't know if I can do this." Lorelai said starting to tear up.

"What do you mean? You have already had one kid and I turned out alright." Rory said hugging her mom.

"But I was so lucky with you. You were so perfect. What if this child, what if I screw it up."

"Mom your not gonna screw it up and look how good I turned out with just you. You have a whole house full of people to help you with baby Danes. Don't worry." Rory said handing her mom a tissue.

"Your right." sniffled Lorelai.

At that point one of the twins started crying. Rory hugged her mom one more time before heading off down stairs to grab a bottle.

4 hours later….

"Rory!" yelled Lorelai running in the door.

"What?" replied Rory with concern.

"I'm having a boy!" Lorelai yelled running up and hugging Rory.

"Oh my gosh! Your having a boy! A boy!" Rory yelled the two jumping up and down screaming and giggling.

"What's going on?" Jess asked stepping into the living room with (6 month old) Lucas on his hip at the same time Luke was coming in.

"Mom is having a boy!" Rory squealed.

"Congrats Luke." Jess smiled patting him on the back.

"Thanks." smiled a proud Luke.

"You know, we should go out and celebrate." Jess said.

"We should. There is that new restaurant in Hartford that I've been dying to try. Can we go Luke?" pouted Lorelai.

"Alright but nun of that pouting stuff, you know I always cave." Luke grumbled walking into the kitchen with Jess.

Later that night….

Since the restaurant was a nicer one both girls took longer to get ready. Rory wore a black dress that had tank top sleeves. Under the chest was a bland of gold/bronze sequence and beads. She also wore a pair of bronze platforms and bronze chandelier earrings. Lorelai wore a blue dress that was free and airy. It had an airy wave on the chest and simple barely there sleeves. She wore simple silver heals and silver jewelry. Their hair and makeup was also simple but very pretty. Jess and Luke were also nicely dressed in some older suit but still very handsome. They had dropped the babies off and Aunt Lane's.

"So what would you like to drink this evening?" asked the waiter.

They all said some sort of soda until he got to Rory who said Martini dry.

"Uhmp." smirked Lorelai.

"What?" asked Rory. "I was pregnant when I turned 21 so I can now drink and I want one."

"Oh know its fine I just realized I can't have any for nine months." Lorelai pouted.

"Welcome to motherhood." smiled Rory lifting her glass in a toast to her mother.

"Ha ha funny." Lorelai glared at her.

After they had eaten their dinner they had all ordered dessert.

"Where is it? We ordered it like 20 minutes ago." Lorelai groaned resting her head in her hands. "I'm gonna go see what's taking them so long." she said standing up.

"I'm going to go with her and make sure she doesn't stab them or something." Luke said stumbling up after her.

"We'll be back." Lorelai said in a sing song voice and winking at Jess.

"What was that all about?" Rory asked looking at Jess.

"Rory how long have we known each other?" Jess asked turning toward Rory.

"Well since we were 16 so 5 years." Rory said not following.

"Exactly and we have been living together as a family since we found out about the twins."

"Yeah?" Rory said still not understanding where this was going.

"Are you happy with how everything is?" asked Jess.

"Yes Jess I am I love it." Rory said tearing up hoping Jess wasn't going to leave her.

"Well I'm not." Jess said looking away from Rory and toward the table.

"What?! Jess are you leaving me?"

Jess didn't say anything, he couldn't. All he could do was look at Rory.

Well that's all for now. Hope you like it. I love cliff hangers!!!! Well at least when I know whats happening next! So r&r and I will update faster.

Much Love,

Alli


	5. Chapter 5

**Disclaimer: **I do not own anything Gilmore Girls

**Chapter 5 **

"_Are you happy with how everything is?" asked Jess._

"_Yes Jess I am I love it." Rory said tearing up hoping Jess wasn't going to leave her._

"_Well I'm not." Jess said looking away from Rory and toward the table._

"_What?! Jess are you leaving me?" _

_Jess didn't say anything, he couldn't. All he could do was look at Rory._

"No! No Rory never! I love you to much!" Jess answered wiping a silent tear from Rory's cheek.

"Than why are you doing this, Jess? Why are you talking this way?" asked a hysteric Rory.

"Look…" he sighed. "I'll be the first to tell you I'm not happy with things the way they are."

"Well why don't I just leave then?" Rory asked grabbing her purse and running towards the exit.

_Over by the counter Luke and Lorelai were watching…._

"Was that supposed to happen?" asked Luke.

"No…Rory!" Lorelai called after her and then followed behind her.


	6. My Knight and His Nobel PickUp

Disclaimer: Again I do not own Gilmore Girls cuz if I did there wouldn't be more than just 7 seasons!

An: WARNING! this may seem like a Rory/Dean chapter but its not and this is still a Rory/Jess story so don't spazz on me ok?

**My Knight and His Nobel Pick-Up**

Rory had no idea where to go. She couldn't leave in the car because the keys where in her coat pocket and her coat was back in the restaurant. She decided shed walk around and look for a taxi. She didn't have money but if she could get a ride to Lane's her childhood friend would loan her some cash. She rubbed her arms from the cold as she walked down the sidewalk. She had stopped crying but her mascara had died in long tear streaks on her cheeks. As she kept walking she heard a familiar noise. She turned her head to she the truck that made her heart stop.

"Dean!?" she whispered.

He must have seen her all along for he pulled the truck to a stop next to the curb. He didn't say anything. He just leaned over and opened the car door for her. She didn't say anything either. She hiked up her dress and slid into the truck.

"Where to?" he asked breaking the silence.

"Lane's" Rory sniffled.

He shook his head in agreement and headed towards Stars Hollow. The whole thirty minute ride was in silence. As he pulled up to Lane's he stopped the truck and turned it off but set in the car. Rory got out and went in after her twins. They were already asleep and in there car seats. Rory quickly thanked Lane and Zach then headed back to the pick-up hoping he hadn't left. She put Lucas in between her and Dean and she held Mary's on her lap. He started the truck but didn't head toward the Gilmore's.

"Uhm…Dean? Where are we going?" Rory asked confused.

"My apartment." he said keeping his eyes on the road.

"No Dean you don't have to do this. Just take me home."

"Fine, I'll take you home so you can grab what you need for you and the babies and leave your mom a quick note that you're fine then you're coming with me."

"Dean…"

"Dang it Rory he's upset you. Come with me so you can cool down that's all."

"Ok." she said a small smile across her face.


	7. Chapter 7

I Don't Own Gilmore Girls

**I Don't Own Gilmore Girls!!**

**What Have I Done?**

Rory woke to knocking. It took her a minute to realize where she was. She was in Dean's bed. She was so glad that Dean had graciously givin her and the twins his bedroom for the night.

"Rory? Are you awake?" Dean mumbled from the other side.

"Just about." she yawned.

"Well you better hurry; you have someone here to see you."

"If it's 'him' tell him to leave." she yelled putting the pillow over her face.

"It's not Jess; it's Lorelai."

"Mom?!" She yelled jumping outta bed long enough to check on the twins to see if they were still asleep and was out of the bedroom in thirty seconds flat. She ran over and hugged her mom taking the coffee in to to-go cup that was marked non-decaf.

"Well I'm going to leave. Lock up when you are done." Dean said walking to the door. "And Rory if you need anything…" He noticed Lorelai's icy stare, shook his head and headed for work.

Rory headed over to sit in the big chair and nursed her coffee while Lorelai sat on the couch drinking her decaf.

"So…."Lorelai looked at her daughter.

Rory bit her bottom lip. "I'm sorry I didn't call!"

"Well you should be. You had me worried sick, Rory. I had no Idea where you or the babies were. When I talked to Lane she said you can and got the twins without a word."

"And Jess?" she whispered looking at the floor.

"He is more crushed than ever. Here it is he planned the most romantic proposal ever and you turned him down. I thought that you wanted to marry him. You don't still have feelings for Dean do you?"

"No…and what he was going to propose?!" Rory said her stomach dropping.

"Uhm yeah."

"Oh my gosh I totally messed this up. Let me grab the twins and let's get outta here." She said running to Dean's bedroom.


	8. Chapter 8

Hey I am having some bad writers block so if you could give me ideas I will add them into the story and I thank you for what i

Hey I am having some bad writers block so if you could give me ideas I will add them into the story and I thank you for what ideas you give me. Thanks!!


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